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Ligand question - aromatic bonds not being enforced?

Submitted by Rick_Baker on Wed, 2019-09-11 09:08
Category: 
Constraints
Small Molecules
Nucleic Acids

Hi,

I am trying to run Local Relax on an ADP-bound protein structure. I cleared the first hurdle to make a ligand params file, and the program runs fine and includes the ligand. I made the params file by taking ADP from a related structure, converted it to mol2 using iBabel, and made the params file using molfile_to_params.py

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Rosetta 3 - General

Options "-out:prefix" didn't work

Submitted by maruhuang on Tue, 2019-09-10 05:42
Category: 
Structure prediction

Hello everyone.

I used AbinitioRelax application to predict structure and added "-out:prefix ab"  into options.

The log shows " protocols.abinitio.AbrelaxApplication: Finished ab_0001 in 169 seconds." but I still got "S_00000001.pdb" file. So I can't simulation on multiple CPUs.

Any help would be appreciate.

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Rosetta 3 - Applications

"Make_fragments.pl" can't connect to dependencies links

Submitted by Corvin on Wed, 2019-09-04 23:54
Category: 
Structure prediction

Dear fellows,

I am studying to generate fragments for structure prediction ab initio locally, on my laptop (OS - Linux OpenSUSE), with a help of appropriate script "make_fragments.pl". I met with several problems during its running.

Firstly, "make_fragments.pl" can not connect to dependencies links. When I run such command, as "~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/make_fragments.pl name.fasta >& make_fragments.local", it gives me such error:

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Rosetta 3 - Applications

antibody protocol fails

Submitted by hamedkhakzad on Mon, 2019-08-19 07:43
Category: 
Structure prediction

Hello,

I'm using antibody protocl to graft some models but it fails with the following error:

File: src/protocols/antibody/grafting/chothia_numberer.cc:152
ERROR: Unxpected length of light-fr3 [length=31], length expected to be: [32, 33, 34]!

Do you have any comments on this? I have three sequences (three different antibodies with light and heavy chains) and it works on one of them but the same error on the two others.

Thanks a lot in advance,

Best

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Rosetta 3 - Applications

Ab initio structure prediction for long amino acid sequence

Submitted by maruhuang on Fri, 2019-08-02 03:38
Category: 
Structure prediction

Hi

I'm a postgraduate student, interested in protein structure prediction.

I noticed that the document said:

  • Abinitio: max 150 amino acids are cosidered possible

So, I want to know, how to use rosetta to predict number of protein of  amino acids more than 150 (e.g. 500)?

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Rosetta 3 - General

Resfile Error

Submitted by ac.research on Wed, 2019-07-17 13:25
Category: 
PyRosetta

Hello everyone,

 

I am trying to perform RosettaDesign, and I have a script that uses pyrosetta.rosetta.core.pack.task.parse_resfile()

In the past this worked just fine, but now with the new update it seems it doesn't work, I get this error: 

RuntimeError:
File: /scratch/benchmark/W.glass/rosetta.Glass/_commits_$ main/source/src/core/pack/task/ResfileReader.cc:1582 [ ERROR ] UtilityExitException ERROR:

I am not sure how to fix this issue, following is two codes that break:

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PyRosetta - General

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